Analysis of the algorithm: From kernels to backup genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
biological_process 1 134 7.052006918351524 11.49779372106138
cellular_component 1 40 4.188809214612387 5.27882174434085
disease 1 21 2.2298934108527133 2.915766749318969
molecular_function 1 26 3.0359319672606953 3.7236643207682025
phenotype 1 335 32.61604938271605 47.760212102568225

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16767x16767 281132289 256626394
cellular_component_sim 17711x17711 313679521 313661810
disease_sim 4128x4128 17040384 16293886
interaction_sim 16098x16098 259145604 479348
molecular_function_sim 17227x17227 296769529 296752302
phenotype_sim 4860x4860 23619600 23614740

Table 3. Filtered similarity matrixes

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process ct 16767x16767 281132289 281132289
biological_process el 16767x16767 281132289 281132289
biological_process ka 16767x16767 281132289 256643161
biological_process rf 16767x16767 281132289 281132289
cellular_component ct 17711x17711 313679521 313679521
cellular_component el 17711x17711 313679521 313679521
cellular_component ka 17711x17711 313679521 313679521
cellular_component rf 17711x17711 313679521 313679521
disease ct 4128x4128 17040384 17040384
disease el 4128x4128 17040384 17032130
disease ka 4128x4128 17040384 16298014
disease rf 4128x4128 17040384 17032130
interaction ct 16098x16098 259145604 259081193
interaction el 16098x16098 259145604 252047984
interaction ka 16098x16098 259145604 495446
interaction rf 16098x16098 259145604 252047984
molecular_function ct 17227x17227 296769529 296769529
molecular_function el 17227x17227 296769529 296769529
molecular_function ka 17227x17227 296769529 296769529
molecular_function rf 17227x17227 296769529 296769529
phenotype ct 4860x4860 23619600 23619600
phenotype el 4860x4860 23619600 23619600
phenotype ka 4860x4860 23619600 23619600
phenotype rf 4860x4860 23619600 23619600

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
integration_mean_by_presence ct 18965x18965 359671225 355593826
integration_mean_by_presence el 18965x18965 359671225 353765394
integration_mean_by_presence ka 18965x18965 359671225 339415588
integration_mean_by_presence rf 18965x18965 359671225 353765394
mean ct 18965x18965 359671225 355593826
mean el 18965x18965 359671225 353765394
mean ka 18965x18965 359671225 339415588
mean rf 18965x18965 359671225 353765394

Weight values